Summarise taxonmic distribution in the EMP dataset
Roey Angel
Biology Centre CAS, Czechiaroey.angel@bc.cas.cz
17 December, 2020
Summarise the taxonmic distribution across different sample types in the Earth Microbiome Project
The Earth Microbiome Project (EMP) is collaborative effort to curate and characterise microbial taxonomy and function on Earth (Thompson et al. 2017).
The aim of this script is to summarise the taxonmic distribution across different sample types, as defined by the EMP. The script summarises phyla by default but can also summarise the sequences at different taxonimc levels. The script uses the 3rd calssification level of the EMP Ontology (empo_3), but this can also be altered.
Set main parameters and download data tables from the EMP FTP site
ftp <- "ftp://ftp.microbio.me/emp/release1/"
biom_file <- "emp_cr_silva_16S_123.subset_10k.biom"
map_file <- "emp_qiime_mapping_subset_10k.tsv"
new_map_file <- "emp_qiime_mapping_subset_10k_noBLNK.csv"
Rank <- "Phylum"
Grouping_var <- "empo_3"
EMPO_levels2keep <- c("Soil (non-saline)", "Plant rhizosphere", "Animal corpus", "Water (saline)", "Sediment (saline)", "Water (non-saline)", "Hypersaline (saline)", "Sediment (non-saline)", "Animal distal gut", "Animal proximal gut", "Aerosol (non-saline)", "Animal secretion", "Animal surface", "Plant corpus", "Surface (non-saline)", "Plant surface", "Surface (saline)") # remove unwanted environmentsbiom_ftp <- paste0(ftp, "otu_tables/closed_ref_silva/", biom_file)
map_ftp <- paste0(ftp, "mapping_files/", map_file)
download.file(biom_ftp, biom_file)
download.file(map_ftp, map_file)
# fill-in missing values with NA, convert to CSV
system("awk 'BEGIN { FS = OFS = \"\t\" } { for(i=1; i<=NF; i++) if($i ~ /^ *$/) $i = \"NA\" }; 1' emp_qiime_mapping_subset_2k.tsv | awk 'BEGIN { FS=\",\"; OFS=\";\" } {$1=$1; print}' | awk 'BEGIN { FS=\"\t\"; OFS=\",\" } {$1=$1; print}' > emp_qiime_mapping_subset_10k_noBLNK.csv")Generate a phyloseq object from the biom and (modified) map files
(EMP_otu_tax <- import_biom(biom_file, parseFunction = parse_taxonomy_silva_128,
parallel = TRUE))## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 126730 taxa and 10000 samples ]:
## tax_table() Taxonomy Table: [ 126730 taxa by 7 taxonomic ranks ]:
## taxa are rowsread_csv(new_map_file,
trim_ws = TRUE) %>%
column_to_rownames("#SampleID") %>%
sample_data() ->
EMP_map
EMP <- merge_phyloseq(EMP_otu_tax, EMP_map)
# for debugging and testing
# EMP %>%
# subset_samples(empo_3 %in% EMPO_levels2keep) %>%
# prune_samples(sample_names(.)[sample(1:nsamples(.), 100)], .) %>%
# phyloseq::filter_taxa(., function(x) sum(x) > 0, TRUE) %>%
# prune_taxa(taxa_names(.)[sample(1:ntaxa(.), 1000)], .) ->
# EMP_subset
EMP %>%
PS_merge_samples(grouping_name = Grouping_var, fun = "mean") ->
EMP_mergeGenerate a summary table of taxonomic distributions across sample types
# summarise abundance by environment and phylum
EMP_merge %>%
tax_glom(taxrank = Rank) %>% # agglomerate at 'Rank' level
psmelt() %>% # Melt to long format
arrange(Rank) %>% # arrange by 'Rank'
group_by_at(c(Grouping_var, Rank)) %>%
# summarise and create a column with the relative abundance
summarise(Abundance = sum(Abundance)) %>%
mutate(Rreq = paste0(round(100 * Abundance / sum(Abundance), 2), "%")) ->
taxa_sum_df
# determine the phylum order by decreasing abundance (for plotting)
EMP_merge %>%
tax_glom(taxrank = Rank) %>% # agglomerate at 'Rank' level
transform_sample_counts(., function(x) x / sum(x) ) %>%
psmelt() %>% # Melt to long format
arrange(Rank) %>% # arrange by 'Rank'
group_by_at(c("OTU", Rank)) %>%
summarise(Abundance = sum(Abundance)) %>%
arrange(Abundance) ->
Rank_order
# print summary table
taxa_sum_df %>%
filter(Abundance != 0) %>%
kable(., digits = c( 0, 1)) %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"), full_width = F)| empo_3 | Phylum | Abundance | Rreq |
|---|---|---|---|
| Aerosol (non-saline) | Acidobacteria | 65715 | 0.8% |
| Aerosol (non-saline) | Actinobacteria | 718035 | 8.73% |
| Aerosol (non-saline) | Aerophobetes | 3 | 0% |
| Aerosol (non-saline) | Aminicenantes | 114 | 0% |
| Aerosol (non-saline) | aquifer1 | 2131 | 0.03% |
| Aerosol (non-saline) | Armatimonadetes | 7036 | 0.09% |
| Aerosol (non-saline) | Atribacteria | 171 | 0% |
| Aerosol (non-saline) | Bacteroidetes | 825065 | 10.03% |
| Aerosol (non-saline) | Caldiserica | 3 | 0% |
| Aerosol (non-saline) | Candidate division OP3 | 149 | 0% |
| Aerosol (non-saline) | Candidate division SR1 | 3317 | 0.04% |
| Aerosol (non-saline) | Chlamydiae | 571 | 0.01% |
| Aerosol (non-saline) | Chlorobi | 645 | 0.01% |
| Aerosol (non-saline) | Chloroflexi | 22528 | 0.27% |
| Aerosol (non-saline) | Cloacimonetes | 349 | 0% |
| Aerosol (non-saline) | Cyanobacteria | 1425687 | 17.33% |
| Aerosol (non-saline) | Deferribacteres | 12 | 0% |
| Aerosol (non-saline) | Deinococcus-Thermus | 2993 | 0.04% |
| Aerosol (non-saline) | Elusimicrobia | 759 | 0.01% |
| Aerosol (non-saline) | Euryarchaeota | 6509 | 0.08% |
| Aerosol (non-saline) | Fibrobacteres | 2681 | 0.03% |
| Aerosol (non-saline) | Firmicutes | 2384579 | 28.98% |
| Aerosol (non-saline) | Fusobacteria | 71051 | 0.86% |
| Aerosol (non-saline) | GAL08 | 1 | 0% |
| Aerosol (non-saline) | Gemmatimonadetes | 17409 | 0.21% |
| Aerosol (non-saline) | Gracilibacteria | 13 | 0% |
| Aerosol (non-saline) | Hyd24-12 | 11 | 0% |
| Aerosol (non-saline) | Hydrogenedentes | 195 | 0% |
| Aerosol (non-saline) | JL-ETNP-Z39 | 28 | 0% |
| Aerosol (non-saline) | Latescibacteria | 189 | 0% |
| Aerosol (non-saline) | Lentisphaerae | 2958 | 0.04% |
| Aerosol (non-saline) | Marinimicrobia (SAR406 clade) | 498 | 0.01% |
| Aerosol (non-saline) | Microgenomates | 3 | 0% |
| Aerosol (non-saline) | Miscellaneous Crenarchaeotic Group | 15 | 0% |
| Aerosol (non-saline) | Nitrospirae | 2424 | 0.03% |
| Aerosol (non-saline) | Omnitrophica | 3 | 0% |
| Aerosol (non-saline) | Parcubacteria | 660 | 0.01% |
| Aerosol (non-saline) | PAUC34f | 2 | 0% |
| Aerosol (non-saline) | Planctomycetes | 17895 | 0.22% |
| Aerosol (non-saline) | Proteobacteria | 2538308 | 30.85% |
| Aerosol (non-saline) | Saccharibacteria | 2235 | 0.03% |
| Aerosol (non-saline) | SHA-109 | 335 | 0% |
| Aerosol (non-saline) | SM2F11 | 5 | 0% |
| Aerosol (non-saline) | Spirochaetae | 14928 | 0.18% |
| Aerosol (non-saline) | Synergistetes | 1844 | 0.02% |
| Aerosol (non-saline) | TA06 | 9 | 0% |
| Aerosol (non-saline) | Tenericutes | 14461 | 0.18% |
| Aerosol (non-saline) | Thaumarchaeota | 6196 | 0.08% |
| Aerosol (non-saline) | Thermotogae | 5877 | 0.07% |
| Aerosol (non-saline) | TM6 | 970 | 0.01% |
| Aerosol (non-saline) | uncultured archaeon | 1 | 0% |
| Aerosol (non-saline) | Verrucomicrobia | 59161 | 0.72% |
| Aerosol (non-saline) | WCHB1-60 | 9 | 0% |
| Aerosol (non-saline) | WD272 | 1656 | 0.02% |
| Aerosol (non-saline) | Woesearchaeota (DHVEG-6) | 2 | 0% |
| Animal corpus | Acetothermia | 47 | 0% |
| Animal corpus | Acidobacteria | 33383 | 0.65% |
| Animal corpus | Actinobacteria | 940836 | 18.35% |
| Animal corpus | Aerophobetes | 243 | 0% |
| Animal corpus | Aminicenantes | 244 | 0% |
| Animal corpus | aquifer1 | 23 | 0% |
| Animal corpus | Aquificae | 12 | 0% |
| Animal corpus | Armatimonadetes | 2576 | 0.05% |
| Animal corpus | Atribacteria | 1014 | 0.02% |
| Animal corpus | Bacteroidetes | 265073 | 5.17% |
| Animal corpus | Caldiserica | 2 | 0% |
| Animal corpus | Candidate division OP3 | 118 | 0% |
| Animal corpus | Candidate division SR1 | 58 | 0% |
| Animal corpus | Chlamydiae | 114 | 0% |
| Animal corpus | Chlorobi | 926 | 0.02% |
| Animal corpus | Chloroflexi | 2474 | 0.05% |
| Animal corpus | Cyanobacteria | 123478 | 2.41% |
| Animal corpus | Deferribacteres | 52 | 0% |
| Animal corpus | Deinococcus-Thermus | 474 | 0.01% |
| Animal corpus | Elusimicrobia | 17 | 0% |
| Animal corpus | Euryarchaeota | 416 | 0.01% |
| Animal corpus | Fibrobacteres | 58 | 0% |
| Animal corpus | Firmicutes | 540593 | 10.54% |
| Animal corpus | Fusobacteria | 9791 | 0.19% |
| Animal corpus | Gemmatimonadetes | 2488 | 0.05% |
| Animal corpus | GOUTA4 | 10 | 0% |
| Animal corpus | Gracilibacteria | 7 | 0% |
| Animal corpus | Hyd24-12 | 54 | 0% |
| Animal corpus | Hydrogenedentes | 40 | 0% |
| Animal corpus | JL-ETNP-Z39 | 20 | 0% |
| Animal corpus | Latescibacteria | 12 | 0% |
| Animal corpus | LCP-89 | 8 | 0% |
| Animal corpus | Lentisphaerae | 29 | 0% |
| Animal corpus | Marinimicrobia (SAR406 clade) | 920 | 0.02% |
| Animal corpus | Microgenomates | 3 | 0% |
| Animal corpus | Miscellaneous Crenarchaeotic Group | 4 | 0% |
| Animal corpus | Nitrospirae | 268 | 0.01% |
| Animal corpus | Parcubacteria | 35 | 0% |
| Animal corpus | Planctomycetes | 1799 | 0.04% |
| Animal corpus | Proteobacteria | 3180203 | 62.02% |
| Animal corpus | Saccharibacteria | 181 | 0% |
| Animal corpus | SHA-109 | 12 | 0% |
| Animal corpus | SM2F11 | 12 | 0% |
| Animal corpus | Spirochaetae | 544 | 0.01% |
| Animal corpus | Synergistetes | 163 | 0% |
| Animal corpus | TA06 | 6 | 0% |
| Animal corpus | Tenericutes | 7571 | 0.15% |
| Animal corpus | Thaumarchaeota | 584 | 0.01% |
| Animal corpus | Thermotogae | 39 | 0% |
| Animal corpus | TM6 | 137 | 0% |
| Animal corpus | Verrucomicrobia | 10794 | 0.21% |
| Animal corpus | WCHB1-60 | 16 | 0% |
| Animal corpus | WD272 | 2 | 0% |
| Animal corpus | Woesearchaeota (DHVEG-6) | 1 | 0% |
| Animal distal gut | Acidobacteria | 1368 | 0.02% |
| Animal distal gut | Actinobacteria | 255935 | 2.81% |
| Animal distal gut | Aerophobetes | 1 | 0% |
| Animal distal gut | Aminicenantes | 6 | 0% |
| Animal distal gut | aquifer1 | 17 | 0% |
| Animal distal gut | Armatimonadetes | 306 | 0% |
| Animal distal gut | Bacteroidetes | 1915725 | 21.05% |
| Animal distal gut | Caldiserica | 6 | 0% |
| Animal distal gut | Candidate division OP3 | 2 | 0% |
| Animal distal gut | Candidate division SR1 | 8 | 0% |
| Animal distal gut | Chlamydiae | 78 | 0% |
| Animal distal gut | Chlorobi | 33 | 0% |
| Animal distal gut | Chloroflexi | 2520 | 0.03% |
| Animal distal gut | CKC4 | 1039 | 0.01% |
| Animal distal gut | Cyanobacteria | 173918 | 1.91% |
| Animal distal gut | Deferribacteres | 42 | 0% |
| Animal distal gut | Deinococcus-Thermus | 306 | 0% |
| Animal distal gut | Elusimicrobia | 1639 | 0.02% |
| Animal distal gut | Euryarchaeota | 29710 | 0.33% |
| Animal distal gut | Fibrobacteres | 3715 | 0.04% |
| Animal distal gut | Firmicutes | 3899629 | 42.84% |
| Animal distal gut | Fusobacteria | 127764 | 1.4% |
| Animal distal gut | Gemmatimonadetes | 117 | 0% |
| Animal distal gut | Gracilibacteria | 252 | 0% |
| Animal distal gut | Hydrogenedentes | 13 | 0% |
| Animal distal gut | Kazan-3B-09 | 1 | 0% |
| Animal distal gut | Latescibacteria | 19 | 0% |
| Animal distal gut | Lentisphaerae | 15139 | 0.17% |
| Animal distal gut | Marinimicrobia (SAR406 clade) | 98 | 0% |
| Animal distal gut | Microgenomates | 9 | 0% |
| Animal distal gut | Miscellaneous Crenarchaeotic Group | 1 | 0% |
| Animal distal gut | Nitrospirae | 82 | 0% |
| Animal distal gut | Omnitrophica | 1 | 0% |
| Animal distal gut | Parcubacteria | 9 | 0% |
| Animal distal gut | Planctomycetes | 17076 | 0.19% |
| Animal distal gut | Proteobacteria | 2414998 | 26.53% |
| Animal distal gut | RsaHF231 | 41 | 0% |
| Animal distal gut | Saccharibacteria | 391 | 0% |
| Animal distal gut | SHA-109 | 273 | 0% |
| Animal distal gut | Spirochaetae | 45267 | 0.5% |
| Animal distal gut | Synergistetes | 1914 | 0.02% |
| Animal distal gut | TA06 | 2 | 0% |
| Animal distal gut | Tenericutes | 93010 | 1.02% |
| Animal distal gut | Thaumarchaeota | 107 | 0% |
| Animal distal gut | TM6 | 49 | 0% |
| Animal distal gut | Verrucomicrobia | 99716 | 1.1% |
| Animal distal gut | WCHB1-60 | 27 | 0% |
| Animal distal gut | WD272 | 4 | 0% |
| Animal distal gut | Woesearchaeota (DHVEG-6) | 2 | 0% |
| Animal proximal gut | Acidobacteria | 2004 | 0.03% |
| Animal proximal gut | Actinobacteria | 522437 | 6.87% |
| Animal proximal gut | aquifer1 | 43 | 0% |
| Animal proximal gut | Aquificae | 5 | 0% |
| Animal proximal gut | Armatimonadetes | 91 | 0% |
| Animal proximal gut | Bacteroidetes | 1588077 | 20.87% |
| Animal proximal gut | Caldiserica | 4 | 0% |
| Animal proximal gut | Candidate division OP3 | 1 | 0% |
| Animal proximal gut | Candidate division SR1 | 282 | 0% |
| Animal proximal gut | Chlamydiae | 78 | 0% |
| Animal proximal gut | Chlorobi | 38 | 0% |
| Animal proximal gut | Chloroflexi | 1631 | 0.02% |
| Animal proximal gut | Cyanobacteria | 198842 | 2.61% |
| Animal proximal gut | Deferribacteres | 112 | 0% |
| Animal proximal gut | Deinococcus-Thermus | 548 | 0.01% |
| Animal proximal gut | Elusimicrobia | 52 | 0% |
| Animal proximal gut | Euryarchaeota | 15879 | 0.21% |
| Animal proximal gut | Fibrobacteres | 14306 | 0.19% |
| Animal proximal gut | Firmicutes | 3358560 | 44.14% |
| Animal proximal gut | Fusobacteria | 11470 | 0.15% |
| Animal proximal gut | Gemmatimonadetes | 601 | 0.01% |
| Animal proximal gut | Gracilibacteria | 32 | 0% |
| Animal proximal gut | Hydrogenedentes | 3 | 0% |
| Animal proximal gut | Latescibacteria | 3 | 0% |
| Animal proximal gut | Lentisphaerae | 9934 | 0.13% |
| Animal proximal gut | Marinimicrobia (SAR406 clade) | 2 | 0% |
| Animal proximal gut | Nitrospirae | 39 | 0% |
| Animal proximal gut | Omnitrophica | 8 | 0% |
| Animal proximal gut | Parcubacteria | 5 | 0% |
| Animal proximal gut | PAUC34f | 1 | 0% |
| Animal proximal gut | Planctomycetes | 89883 | 1.18% |
| Animal proximal gut | Proteobacteria | 1371070 | 18.02% |
| Animal proximal gut | Saccharibacteria | 57 | 0% |
| Animal proximal gut | SHA-109 | 337 | 0% |
| Animal proximal gut | SM2F11 | 1 | 0% |
| Animal proximal gut | Spirochaetae | 137338 | 1.8% |
| Animal proximal gut | Synergistetes | 2241 | 0.03% |
| Animal proximal gut | Tenericutes | 21776 | 0.29% |
| Animal proximal gut | Thaumarchaeota | 568 | 0.01% |
| Animal proximal gut | Thermotogae | 4 | 0% |
| Animal proximal gut | TM6 | 56 | 0% |
| Animal proximal gut | Verrucomicrobia | 261203 | 3.43% |
| Animal proximal gut | WCHB1-60 | 5 | 0% |
| Animal proximal gut | WD272 | 80 | 0% |
| Animal proximal gut | Woesearchaeota (DHVEG-6) | 35 | 0% |
| Animal secretion | Acidobacteria | 7412 | 0.1% |
| Animal secretion | Actinobacteria | 750903 | 10.03% |
| Animal secretion | Aerophobetes | 1 | 0% |
| Animal secretion | Aminicenantes | 32 | 0% |
| Animal secretion | aquifer1 | 7206 | 0.1% |
| Animal secretion | Armatimonadetes | 604 | 0.01% |
| Animal secretion | Bacteroidetes | 982127 | 13.12% |
| Animal secretion | Candidate division OP3 | 2 | 0% |
| Animal secretion | Candidate division SR1 | 4813 | 0.06% |
| Animal secretion | Chlamydiae | 781 | 0.01% |
| Animal secretion | Chlorobi | 683 | 0.01% |
| Animal secretion | Chloroflexi | 5634 | 0.08% |
| Animal secretion | Crenarchaeota | 1 | 0% |
| Animal secretion | Cyanobacteria | 46048 | 0.62% |
| Animal secretion | Deferribacteres | 48 | 0% |
| Animal secretion | Deinococcus-Thermus | 5777 | 0.08% |
| Animal secretion | Elusimicrobia | 36 | 0% |
| Animal secretion | Euryarchaeota | 842 | 0.01% |
| Animal secretion | Fibrobacteres | 21 | 0% |
| Animal secretion | Firmicutes | 2390653 | 31.94% |
| Animal secretion | Fusobacteria | 309677 | 4.14% |
| Animal secretion | Gemmatimonadetes | 3799 | 0.05% |
| Animal secretion | GOUTA4 | 2 | 0% |
| Animal secretion | Gracilibacteria | 917 | 0.01% |
| Animal secretion | Hydrogenedentes | 241 | 0% |
| Animal secretion | JL-ETNP-Z39 | 17 | 0% |
| Animal secretion | Latescibacteria | 56 | 0% |
| Animal secretion | LCP-89 | 1 | 0% |
| Animal secretion | Lentisphaerae | 162 | 0% |
| Animal secretion | Marinimicrobia (SAR406 clade) | 471 | 0.01% |
| Animal secretion | Microgenomates | 49 | 0% |
| Animal secretion | Miscellaneous Crenarchaeotic Group | 17 | 0% |
| Animal secretion | Nitrospirae | 786 | 0.01% |
| Animal secretion | OC31 | 1 | 0% |
| Animal secretion | Omnitrophica | 1 | 0% |
| Animal secretion | Parcubacteria | 160 | 0% |
| Animal secretion | PAUC34f | 2 | 0% |
| Animal secretion | Planctomycetes | 3125 | 0.04% |
| Animal secretion | Proteobacteria | 2792267 | 37.3% |
| Animal secretion | Saccharibacteria | 6599 | 0.09% |
| Animal secretion | SHA-109 | 31 | 0% |
| Animal secretion | SM2F11 | 15 | 0% |
| Animal secretion | Spirochaetae | 7108 | 0.09% |
| Animal secretion | Synergistetes | 967 | 0.01% |
| Animal secretion | TA06 | 17 | 0% |
| Animal secretion | Tenericutes | 148187 | 1.98% |
| Animal secretion | Thaumarchaeota | 627 | 0.01% |
| Animal secretion | TM6 | 61 | 0% |
| Animal secretion | Verrucomicrobia | 6691 | 0.09% |
| Animal secretion | WCHB1-60 | 29 | 0% |
| Animal secretion | WD272 | 25 | 0% |
| Animal secretion | Woesearchaeota (DHVEG-6) | 18 | 0% |
| Animal surface | Acidobacteria | 22815 | 0.24% |
| Animal surface | Actinobacteria | 1195171 | 12.54% |
| Animal surface | Aerophobetes | 2 | 0% |
| Animal surface | Aminicenantes | 13 | 0% |
| Animal surface | aquifer1 | 797 | 0.01% |
| Animal surface | Armatimonadetes | 4434 | 0.05% |
| Animal surface | Atribacteria | 29 | 0% |
| Animal surface | Bacteroidetes | 939832 | 9.86% |
| Animal surface | Caldiserica | 4 | 0% |
| Animal surface | Candidate division OP3 | 13 | 0% |
| Animal surface | Candidate division SR1 | 796 | 0.01% |
| Animal surface | Chlamydiae | 334 | 0% |
| Animal surface | Chlorobi | 908 | 0.01% |
| Animal surface | Chloroflexi | 10418 | 0.11% |
| Animal surface | CKC4 | 26 | 0% |
| Animal surface | Cloacimonetes | 4 | 0% |
| Animal surface | Cyanobacteria | 208679 | 2.19% |
| Animal surface | Deferribacteres | 72 | 0% |
| Animal surface | Deinococcus-Thermus | 8109 | 0.09% |
| Animal surface | Elusimicrobia | 157 | 0% |
| Animal surface | Euryarchaeota | 937 | 0.01% |
| Animal surface | Fibrobacteres | 157 | 0% |
| Animal surface | Firmicutes | 1931918 | 20.27% |
| Animal surface | Fusobacteria | 107148 | 1.12% |
| Animal surface | GAL08 | 1 | 0% |
| Animal surface | Gemmatimonadetes | 8330 | 0.09% |
| Animal surface | GOUTA4 | 1 | 0% |
| Animal surface | Gracilibacteria | 360 | 0% |
| Animal surface | Hydrogenedentes | 500 | 0.01% |
| Animal surface | JL-ETNP-Z39 | 17 | 0% |
| Animal surface | Latescibacteria | 170 | 0% |
| Animal surface | LCP-89 | 1 | 0% |
| Animal surface | Lentisphaerae | 946 | 0.01% |
| Animal surface | Marine Hydrothermal Vent Group(MHVG) | 5 | 0% |
| Animal surface | Marinimicrobia (SAR406 clade) | 42 | 0% |
| Animal surface | Microgenomates | 11 | 0% |
| Animal surface | Miscellaneous Crenarchaeotic Group | 17 | 0% |
| Animal surface | Nitrospirae | 1271 | 0.01% |
| Animal surface | OC31 | 1 | 0% |
| Animal surface | Omnitrophica | 48 | 0% |
| Animal surface | Parcubacteria | 45 | 0% |
| Animal surface | PAUC34f | 186 | 0% |
| Animal surface | Planctomycetes | 11390 | 0.12% |
| Animal surface | Proteobacteria | 4884024 | 51.25% |
| Animal surface | RsaHF231 | 11 | 0% |
| Animal surface | Saccharibacteria | 433 | 0% |
| Animal surface | SHA-109 | 688 | 0.01% |
| Animal surface | SM2F11 | 8 | 0% |
| Animal surface | Spirochaetae | 2301 | 0.02% |
| Animal surface | Synergistetes | 351 | 0% |
| Animal surface | TA06 | 188 | 0% |
| Animal surface | Tenericutes | 153480 | 1.61% |
| Animal surface | Thaumarchaeota | 1351 | 0.01% |
| Animal surface | Thermotogae | 17 | 0% |
| Animal surface | TM6 | 239 | 0% |
| Animal surface | uncultured archaeon | 1 | 0% |
| Animal surface | Verrucomicrobia | 30320 | 0.32% |
| Animal surface | WCHB1-60 | 158 | 0% |
| Animal surface | WD272 | 161 | 0% |
| Animal surface | Woesearchaeota (DHVEG-6) | 17 | 0% |
| Hypersaline (saline) | Acetothermia | 3106 | 0.34% |
| Hypersaline (saline) | Acidobacteria | 19360 | 2.09% |
| Hypersaline (saline) | Actinobacteria | 47574 | 5.15% |
| Hypersaline (saline) | Aenigmarchaeota | 210 | 0.02% |
| Hypersaline (saline) | Aerophobetes | 77 | 0.01% |
| Hypersaline (saline) | Aminicenantes | 1274 | 0.14% |
| Hypersaline (saline) | Armatimonadetes | 1078 | 0.12% |
| Hypersaline (saline) | Atribacteria | 82 | 0.01% |
| Hypersaline (saline) | Bacteroidetes | 114614 | 12.4% |
| Hypersaline (saline) | Caldiserica | 1 | 0% |
| Hypersaline (saline) | Candidate division OP3 | 364 | 0.04% |
| Hypersaline (saline) | Candidate division SR1 | 34 | 0% |
| Hypersaline (saline) | Chlamydiae | 15 | 0% |
| Hypersaline (saline) | Chlorobi | 462 | 0.05% |
| Hypersaline (saline) | Chloroflexi | 18848 | 2.04% |
| Hypersaline (saline) | Cloacimonetes | 26 | 0% |
| Hypersaline (saline) | Crenarchaeota | 1 | 0% |
| Hypersaline (saline) | Cyanobacteria | 8149 | 0.88% |
| Hypersaline (saline) | Deferribacteres | 394 | 0.04% |
| Hypersaline (saline) | Deinococcus-Thermus | 4400 | 0.48% |
| Hypersaline (saline) | Elusimicrobia | 107 | 0.01% |
| Hypersaline (saline) | Euryarchaeota | 304473 | 32.95% |
| Hypersaline (saline) | Fibrobacteres | 330 | 0.04% |
| Hypersaline (saline) | Firmicutes | 6631 | 0.72% |
| Hypersaline (saline) | Fusobacteria | 77 | 0.01% |
| Hypersaline (saline) | GAL08 | 1 | 0% |
| Hypersaline (saline) | Gemmatimonadetes | 4860 | 0.53% |
| Hypersaline (saline) | Gracilibacteria | 119 | 0.01% |
| Hypersaline (saline) | Hyd24-12 | 508 | 0.05% |
| Hypersaline (saline) | Hydrogenedentes | 165 | 0.02% |
| Hypersaline (saline) | JL-ETNP-Z39 | 27 | 0% |
| Hypersaline (saline) | Kazan-3B-09 | 5 | 0% |
| Hypersaline (saline) | Latescibacteria | 1358 | 0.15% |
| Hypersaline (saline) | LCP-89 | 80 | 0.01% |
| Hypersaline (saline) | LD1-PA38 | 6 | 0% |
| Hypersaline (saline) | Lentisphaerae | 3160 | 0.34% |
| Hypersaline (saline) | Marinimicrobia (SAR406 clade) | 1611 | 0.17% |
| Hypersaline (saline) | Microgenomates | 29 | 0% |
| Hypersaline (saline) | Miscellaneous Crenarchaeotic Group | 279 | 0.03% |
| Hypersaline (saline) | Nanohaloarchaeota | 1761 | 0.19% |
| Hypersaline (saline) | Nitrospirae | 1651 | 0.18% |
| Hypersaline (saline) | Omnitrophica | 306 | 0.03% |
| Hypersaline (saline) | Parcubacteria | 400 | 0.04% |
| Hypersaline (saline) | PAUC34f | 147 | 0.02% |
| Hypersaline (saline) | Planctomycetes | 12674 | 1.37% |
| Hypersaline (saline) | Proteobacteria | 333511 | 36.09% |
| Hypersaline (saline) | Saccharibacteria | 1 | 0% |
| Hypersaline (saline) | SHA-109 | 14 | 0% |
| Hypersaline (saline) | Spirochaetae | 5920 | 0.64% |
| Hypersaline (saline) | TA06 | 1053 | 0.11% |
| Hypersaline (saline) | Tenericutes | 13494 | 1.46% |
| Hypersaline (saline) | Thaumarchaeota | 5658 | 0.61% |
| Hypersaline (saline) | Thermotogae | 12 | 0% |
| Hypersaline (saline) | TM6 | 59 | 0.01% |
| Hypersaline (saline) | Verrucomicrobia | 2701 | 0.29% |
| Hypersaline (saline) | WD272 | 2 | 0% |
| Hypersaline (saline) | Woesearchaeota (DHVEG-6) | 920 | 0.1% |
| Plant corpus | Acetothermia | 11 | 0% |
| Plant corpus | Acidobacteria | 11648 | 0.07% |
| Plant corpus | Actinobacteria | 403923 | 2.53% |
| Plant corpus | Aerophobetes | 140 | 0% |
| Plant corpus | Aminicenantes | 218 | 0% |
| Plant corpus | aquifer1 | 9 | 0% |
| Plant corpus | Aquificae | 1 | 0% |
| Plant corpus | Armatimonadetes | 1494 | 0.01% |
| Plant corpus | Atribacteria | 291 | 0% |
| Plant corpus | Bacteroidetes | 160603 | 1.01% |
| Plant corpus | Candidate division OP3 | 21 | 0% |
| Plant corpus | Candidate division SR1 | 15 | 0% |
| Plant corpus | Chlamydiae | 48 | 0% |
| Plant corpus | Chlorobi | 139 | 0% |
| Plant corpus | Chloroflexi | 3944 | 0.02% |
| Plant corpus | Cyanobacteria | 12360725 | 77.48% |
| Plant corpus | Deferribacteres | 34 | 0% |
| Plant corpus | Deinococcus-Thermus | 1869 | 0.01% |
| Plant corpus | Elusimicrobia | 8 | 0% |
| Plant corpus | Euryarchaeota | 293 | 0% |
| Plant corpus | Fibrobacteres | 71 | 0% |
| Plant corpus | Firmicutes | 177325 | 1.11% |
| Plant corpus | Fusobacteria | 12825 | 0.08% |
| Plant corpus | Gemmatimonadetes | 1787 | 0.01% |
| Plant corpus | Gracilibacteria | 15 | 0% |
| Plant corpus | Hydrogenedentes | 122 | 0% |
| Plant corpus | JL-ETNP-Z39 | 21 | 0% |
| Plant corpus | Latescibacteria | 14 | 0% |
| Plant corpus | Lentisphaerae | 25 | 0% |
| Plant corpus | Marinimicrobia (SAR406 clade) | 11 | 0% |
| Plant corpus | Microgenomates | 11 | 0% |
| Plant corpus | Miscellaneous Crenarchaeotic Group | 8 | 0% |
| Plant corpus | Nitrospirae | 427 | 0% |
| Plant corpus | Omnitrophica | 40 | 0% |
| Plant corpus | Parcubacteria | 2 | 0% |
| Plant corpus | Planctomycetes | 3647 | 0.02% |
| Plant corpus | Proteobacteria | 2799980 | 17.55% |
| Plant corpus | Saccharibacteria | 246 | 0% |
| Plant corpus | SHA-109 | 28 | 0% |
| Plant corpus | SM2F11 | 1 | 0% |
| Plant corpus | Spirochaetae | 207 | 0% |
| Plant corpus | Synergistetes | 41 | 0% |
| Plant corpus | TA06 | 6 | 0% |
| Plant corpus | Tenericutes | 3237 | 0.02% |
| Plant corpus | Thaumarchaeota | 3763 | 0.02% |
| Plant corpus | Thermotogae | 1 | 0% |
| Plant corpus | TM6 | 37 | 0% |
| Plant corpus | Verrucomicrobia | 3973 | 0.02% |
| Plant corpus | WCHB1-60 | 34 | 0% |
| Plant corpus | WD272 | 1 | 0% |
| Plant corpus | Woesearchaeota (DHVEG-6) | 2 | 0% |
| Plant rhizosphere | Acidobacteria | 1845110 | 14.46% |
| Plant rhizosphere | Actinobacteria | 591199 | 4.63% |
| Plant rhizosphere | Aenigmarchaeota | 369 | 0% |
| Plant rhizosphere | Aerophobetes | 391 | 0% |
| Plant rhizosphere | Aminicenantes | 2904 | 0.02% |
| Plant rhizosphere | Armatimonadetes | 53517 | 0.42% |
| Plant rhizosphere | Atribacteria | 1 | 0% |
| Plant rhizosphere | Bacteroidetes | 1274309 | 9.99% |
| Plant rhizosphere | Caldiserica | 334 | 0% |
| Plant rhizosphere | Candidate division OP3 | 7632 | 0.06% |
| Plant rhizosphere | Candidate division SR1 | 504 | 0% |
| Plant rhizosphere | Chlamydiae | 4828 | 0.04% |
| Plant rhizosphere | Chlorobi | 146367 | 1.15% |
| Plant rhizosphere | Chloroflexi | 553957 | 4.34% |
| Plant rhizosphere | CKC4 | 2 | 0% |
| Plant rhizosphere | Cloacimonetes | 186 | 0% |
| Plant rhizosphere | Cyanobacteria | 422028 | 3.31% |
| Plant rhizosphere | Deferribacteres | 316 | 0% |
| Plant rhizosphere | Deinococcus-Thermus | 4420 | 0.03% |
| Plant rhizosphere | Diapherotrites | 4 | 0% |
| Plant rhizosphere | Dictyoglomi | 2 | 0% |
| Plant rhizosphere | Elusimicrobia | 28048 | 0.22% |
| Plant rhizosphere | Euryarchaeota | 105898 | 0.83% |
| Plant rhizosphere | Fibrobacteres | 19751 | 0.15% |
| Plant rhizosphere | Firmicutes | 264820 | 2.08% |
| Plant rhizosphere | Fusobacteria | 615 | 0% |
| Plant rhizosphere | GAL08 | 120 | 0% |
| Plant rhizosphere | Gemmatimonadetes | 193921 | 1.52% |
| Plant rhizosphere | GOUTA4 | 5137 | 0.04% |
| Plant rhizosphere | Gracilibacteria | 1531 | 0.01% |
| Plant rhizosphere | Hydrogenedentes | 4302 | 0.03% |
| Plant rhizosphere | JL-ETNP-Z39 | 432 | 0% |
| Plant rhizosphere | Kazan-3B-09 | 48 | 0% |
| Plant rhizosphere | Latescibacteria | 41768 | 0.33% |
| Plant rhizosphere | Lentisphaerae | 4903 | 0.04% |
| Plant rhizosphere | Marine Hydrothermal Vent Group(MHVG) | 17 | 0% |
| Plant rhizosphere | Marinimicrobia (SAR406 clade) | 142 | 0% |
| Plant rhizosphere | Microgenomates | 2187 | 0.02% |
| Plant rhizosphere | Miscellaneous Crenarchaeotic Group | 18573 | 0.15% |
| Plant rhizosphere | Miscellaneous Euryarchaeotic Group(MEG) | 32 | 0% |
| Plant rhizosphere | Nitrospirae | 187989 | 1.47% |
| Plant rhizosphere | OC31 | 10 | 0% |
| Plant rhizosphere | Omnitrophica | 6420 | 0.05% |
| Plant rhizosphere | Parcubacteria | 5648 | 0.04% |
| Plant rhizosphere | Parvarchaeota | 829 | 0.01% |
| Plant rhizosphere | PAUC34f | 228 | 0% |
| Plant rhizosphere | Planctomycetes | 313880 | 2.46% |
| Plant rhizosphere | Proteobacteria | 5742756 | 45.02% |
| Plant rhizosphere | Saccharibacteria | 883 | 0.01% |
| Plant rhizosphere | SHA-109 | 465 | 0% |
| Plant rhizosphere | SM1K20 | 774 | 0.01% |
| Plant rhizosphere | SM2F11 | 2753 | 0.02% |
| Plant rhizosphere | Spirochaetae | 64318 | 0.5% |
| Plant rhizosphere | Synergistetes | 26 | 0% |
| Plant rhizosphere | TA06 | 4950 | 0.04% |
| Plant rhizosphere | Tenericutes | 265 | 0% |
| Plant rhizosphere | Thaumarchaeota | 75252 | 0.59% |
| Plant rhizosphere | Thermotogae | 306 | 0% |
| Plant rhizosphere | TM6 | 3307 | 0.03% |
| Plant rhizosphere | Verrucomicrobia | 733698 | 5.75% |
| Plant rhizosphere | WCHB1-60 | 2797 | 0.02% |
| Plant rhizosphere | WD272 | 87 | 0% |
| Plant rhizosphere | Woesearchaeota (DHVEG-6) | 8614 | 0.07% |
| Plant surface | Acidobacteria | 72806 | 0.56% |
| Plant surface | Actinobacteria | 588202 | 4.53% |
| Plant surface | Aerophobetes | 29 | 0% |
| Plant surface | Armatimonadetes | 1164 | 0.01% |
| Plant surface | Atribacteria | 1 | 0% |
| Plant surface | Bacteroidetes | 2114039 | 16.27% |
| Plant surface | Candidate division OP3 | 34 | 0% |
| Plant surface | Candidate division SR1 | 68 | 0% |
| Plant surface | Chlamydiae | 243 | 0% |
| Plant surface | Chlorobi | 664 | 0.01% |
| Plant surface | Chloroflexi | 22062 | 0.17% |
| Plant surface | Cloacimonetes | 1 | 0% |
| Plant surface | Cyanobacteria | 741341 | 5.71% |
| Plant surface | Deferribacteres | 11 | 0% |
| Plant surface | Deinococcus-Thermus | 13449 | 0.1% |
| Plant surface | Elusimicrobia | 736 | 0.01% |
| Plant surface | Euryarchaeota | 336 | 0% |
| Plant surface | Fibrobacteres | 87 | 0% |
| Plant surface | Firmicutes | 48050 | 0.37% |
| Plant surface | Fusobacteria | 4605 | 0.04% |
| Plant surface | Gemmatimonadetes | 16626 | 0.13% |
| Plant surface | Gracilibacteria | 3973 | 0.03% |
| Plant surface | Hydrogenedentes | 16 | 0% |
| Plant surface | JL-ETNP-Z39 | 3 | 0% |
| Plant surface | Latescibacteria | 2228 | 0.02% |
| Plant surface | Lentisphaerae | 497 | 0% |
| Plant surface | Marinimicrobia (SAR406 clade) | 81 | 0% |
| Plant surface | Microgenomates | 15 | 0% |
| Plant surface | Nitrospirae | 3109 | 0.02% |
| Plant surface | Omnitrophica | 128 | 0% |
| Plant surface | Parcubacteria | 287 | 0% |
| Plant surface | PAUC34f | 27 | 0% |
| Plant surface | Planctomycetes | 824288 | 6.34% |
| Plant surface | Proteobacteria | 7736640 | 59.55% |
| Plant surface | Saccharibacteria | 32 | 0% |
| Plant surface | SHA-109 | 667 | 0.01% |
| Plant surface | SM2F11 | 76 | 0% |
| Plant surface | Spirochaetae | 77 | 0% |
| Plant surface | Synergistetes | 1 | 0% |
| Plant surface | TA06 | 1 | 0% |
| Plant surface | Tenericutes | 53 | 0% |
| Plant surface | Thaumarchaeota | 4756 | 0.04% |
| Plant surface | Thermotogae | 10 | 0% |
| Plant surface | TM6 | 238 | 0% |
| Plant surface | Verrucomicrobia | 789613 | 6.08% |
| Plant surface | WCHB1-60 | 107 | 0% |
| Plant surface | WD272 | 18 | 0% |
| Plant surface | Woesearchaeota (DHVEG-6) | 11 | 0% |
| Sediment (non-saline) | Acetothermia | 88 | 0% |
| Sediment (non-saline) | Acidobacteria | 756499 | 9.23% |
| Sediment (non-saline) | Actinobacteria | 359605 | 4.39% |
| Sediment (non-saline) | Aenigmarchaeota | 16721 | 0.2% |
| Sediment (non-saline) | Aerophobetes | 307 | 0% |
| Sediment (non-saline) | Aminicenantes | 60421 | 0.74% |
| Sediment (non-saline) | aquifer1 | 4 | 0% |
| Sediment (non-saline) | Aquificae | 2 | 0% |
| Sediment (non-saline) | Armatimonadetes | 17176 | 0.21% |
| Sediment (non-saline) | Atribacteria | 6934 | 0.08% |
| Sediment (non-saline) | Bacteroidetes | 582641 | 7.11% |
| Sediment (non-saline) | Caldiserica | 550 | 0.01% |
| Sediment (non-saline) | Candidate division OP3 | 39051 | 0.48% |
| Sediment (non-saline) | Candidate division SR1 | 621 | 0.01% |
| Sediment (non-saline) | Chlamydiae | 1673 | 0.02% |
| Sediment (non-saline) | Chlorobi | 94785 | 1.16% |
| Sediment (non-saline) | Chloroflexi | 405243 | 4.94% |
| Sediment (non-saline) | CKC4 | 84 | 0% |
| Sediment (non-saline) | Cloacimonetes | 202 | 0% |
| Sediment (non-saline) | Crenarchaeota | 6941 | 0.08% |
| Sediment (non-saline) | Cyanobacteria | 181583 | 2.21% |
| Sediment (non-saline) | Deferribacteres | 33172 | 0.4% |
| Sediment (non-saline) | Deinococcus-Thermus | 9001 | 0.11% |
| Sediment (non-saline) | Diapherotrites | 24 | 0% |
| Sediment (non-saline) | Dictyoglomi | 1 | 0% |
| Sediment (non-saline) | Elusimicrobia | 12935 | 0.16% |
| Sediment (non-saline) | Euryarchaeota | 151630 | 1.85% |
| Sediment (non-saline) | Fibrobacteres | 5761 | 0.07% |
| Sediment (non-saline) | Firmicutes | 152958 | 1.87% |
| Sediment (non-saline) | Fusobacteria | 272 | 0% |
| Sediment (non-saline) | GAL08 | 191 | 0% |
| Sediment (non-saline) | Gemmatimonadetes | 134999 | 1.65% |
| Sediment (non-saline) | GOUTA4 | 2663 | 0.03% |
| Sediment (non-saline) | Gracilibacteria | 1910 | 0.02% |
| Sediment (non-saline) | Hyd24-12 | 120 | 0% |
| Sediment (non-saline) | Hydrogenedentes | 4142 | 0.05% |
| Sediment (non-saline) | JL-ETNP-Z39 | 677 | 0.01% |
| Sediment (non-saline) | Kazan-3B-09 | 850 | 0.01% |
| Sediment (non-saline) | Latescibacteria | 43904 | 0.54% |
| Sediment (non-saline) | LCP-89 | 182 | 0% |
| Sediment (non-saline) | LD1-PA38 | 9 | 0% |
| Sediment (non-saline) | Lentisphaerae | 11508 | 0.14% |
| Sediment (non-saline) | Marine Hydrothermal Vent Group(MHVG) | 86 | 0% |
| Sediment (non-saline) | Marinimicrobia (SAR406 clade) | 1163 | 0.01% |
| Sediment (non-saline) | Microgenomates | 699 | 0.01% |
| Sediment (non-saline) | Miscellaneous Crenarchaeotic Group | 173745 | 2.12% |
| Sediment (non-saline) | Miscellaneous Euryarchaeotic Group(MEG) | 332 | 0% |
| Sediment (non-saline) | Nitrospirae | 292186 | 3.56% |
| Sediment (non-saline) | OC31 | 2465 | 0.03% |
| Sediment (non-saline) | Omnitrophica | 6774 | 0.08% |
| Sediment (non-saline) | Parcubacteria | 4000 | 0.05% |
| Sediment (non-saline) | Parvarchaeota | 100 | 0% |
| Sediment (non-saline) | PAUC34f | 1483 | 0.02% |
| Sediment (non-saline) | Planctomycetes | 216888 | 2.65% |
| Sediment (non-saline) | Proteobacteria | 3919770 | 47.81% |
| Sediment (non-saline) | Saccharibacteria | 194 | 0% |
| Sediment (non-saline) | SHA-109 | 802 | 0.01% |
| Sediment (non-saline) | SM1K20 | 1308 | 0.02% |
| Sediment (non-saline) | SM2F11 | 520 | 0.01% |
| Sediment (non-saline) | Spirochaetae | 25867 | 0.32% |
| Sediment (non-saline) | Synergistetes | 386 | 0% |
| Sediment (non-saline) | TA06 | 38984 | 0.48% |
| Sediment (non-saline) | Tenericutes | 837 | 0.01% |
| Sediment (non-saline) | Thaumarchaeota | 71512 | 0.87% |
| Sediment (non-saline) | Thermotogae | 35 | 0% |
| Sediment (non-saline) | TM6 | 3220 | 0.04% |
| Sediment (non-saline) | uncultured archaeon | 32 | 0% |
| Sediment (non-saline) | Verrucomicrobia | 321911 | 3.93% |
| Sediment (non-saline) | WCHB1-60 | 717 | 0.01% |
| Sediment (non-saline) | WD272 | 1612 | 0.02% |
| Sediment (non-saline) | Woesearchaeota (DHVEG-6) | 12906 | 0.16% |
| Sediment (saline) | Acetothermia | 1247 | 0.01% |
| Sediment (saline) | Acidobacteria | 590604 | 4.29% |
| Sediment (saline) | Actinobacteria | 327052 | 2.38% |
| Sediment (saline) | Aenigmarchaeota | 329 | 0% |
| Sediment (saline) | Aerophobetes | 35502 | 0.26% |
| Sediment (saline) | Aigarchaeota | 21 | 0% |
| Sediment (saline) | Aminicenantes | 24317 | 0.18% |
| Sediment (saline) | Ancient Archaeal Group(AAG) | 1347 | 0.01% |
| Sediment (saline) | aquifer1 | 2140 | 0.02% |
| Sediment (saline) | Armatimonadetes | 7397 | 0.05% |
| Sediment (saline) | Atribacteria | 983436 | 7.15% |
| Sediment (saline) | Bacteroidetes | 1490460 | 10.83% |
| Sediment (saline) | Caldiserica | 326 | 0% |
| Sediment (saline) | Candidate division OP3 | 12604 | 0.09% |
| Sediment (saline) | Candidate division SR1 | 1575 | 0.01% |
| Sediment (saline) | Chlamydiae | 2675 | 0.02% |
| Sediment (saline) | Chlorobi | 50015 | 0.36% |
| Sediment (saline) | Chloroflexi | 380903 | 2.77% |
| Sediment (saline) | Chrysiogenetes | 1 | 0% |
| Sediment (saline) | CKC4 | 19 | 0% |
| Sediment (saline) | Cloacimonetes | 3226 | 0.02% |
| Sediment (saline) | Crenarchaeota | 1 | 0% |
| Sediment (saline) | Cyanobacteria | 245168 | 1.78% |
| Sediment (saline) | Deferribacteres | 27461 | 0.2% |
| Sediment (saline) | Deinococcus-Thermus | 6808 | 0.05% |
| Sediment (saline) | Diapherotrites | 33 | 0% |
| Sediment (saline) | Dictyoglomi | 4 | 0% |
| Sediment (saline) | Elusimicrobia | 5105 | 0.04% |
| Sediment (saline) | Euryarchaeota | 157748 | 1.15% |
| Sediment (saline) | Fibrobacteres | 7873 | 0.06% |
| Sediment (saline) | Firmicutes | 444452 | 3.23% |
| Sediment (saline) | Fusobacteria | 24249 | 0.18% |
| Sediment (saline) | GAL08 | 4 | 0% |
| Sediment (saline) | Gemmatimonadetes | 76145 | 0.55% |
| Sediment (saline) | GOUTA4 | 311 | 0% |
| Sediment (saline) | Gracilibacteria | 6211 | 0.05% |
| Sediment (saline) | Hyd24-12 | 8991 | 0.07% |
| Sediment (saline) | Hydrogenedentes | 7288 | 0.05% |
| Sediment (saline) | JL-ETNP-Z39 | 708 | 0.01% |
| Sediment (saline) | Kazan-3B-09 | 1497 | 0.01% |
| Sediment (saline) | Latescibacteria | 51000 | 0.37% |
| Sediment (saline) | LCP-89 | 1100 | 0.01% |
| Sediment (saline) | LD1-PA38 | 247 | 0% |
| Sediment (saline) | Lentisphaerae | 55618 | 0.4% |
| Sediment (saline) | Marine Hydrothermal Vent Group(MHVG) | 2390 | 0.02% |
| Sediment (saline) | Marinimicrobia (SAR406 clade) | 18059 | 0.13% |
| Sediment (saline) | Microgenomates | 2871 | 0.02% |
| Sediment (saline) | Miscellaneous Crenarchaeotic Group | 6267 | 0.05% |
| Sediment (saline) | Miscellaneous Euryarchaeotic Group(MEG) | 19 | 0% |
| Sediment (saline) | Nanohaloarchaeota | 173 | 0% |
| Sediment (saline) | Nitrospirae | 44673 | 0.32% |
| Sediment (saline) | OC31 | 252 | 0% |
| Sediment (saline) | Omnitrophica | 5867 | 0.04% |
| Sediment (saline) | Parcubacteria | 7781 | 0.06% |
| Sediment (saline) | Parvarchaeota | 2 | 0% |
| Sediment (saline) | PAUC34f | 3410 | 0.02% |
| Sediment (saline) | Planctomycetes | 216790 | 1.58% |
| Sediment (saline) | Proteobacteria | 7667735 | 55.72% |
| Sediment (saline) | RsaHF231 | 6 | 0% |
| Sediment (saline) | Saccharibacteria | 348 | 0% |
| Sediment (saline) | SBYG-2791 | 5 | 0% |
| Sediment (saline) | SHA-109 | 1435 | 0.01% |
| Sediment (saline) | SM1K20 | 14 | 0% |
| Sediment (saline) | SM2F11 | 305 | 0% |
| Sediment (saline) | Spirochaetae | 71715 | 0.52% |
| Sediment (saline) | Synergistetes | 530 | 0% |
| Sediment (saline) | TA06 | 16875 | 0.12% |
| Sediment (saline) | Tenericutes | 16848 | 0.12% |
| Sediment (saline) | Thaumarchaeota | 183805 | 1.34% |
| Sediment (saline) | Thermotogae | 223 | 0% |
| Sediment (saline) | TM6 | 4990 | 0.04% |
| Sediment (saline) | uncultured archaeon | 1217 | 0.01% |
| Sediment (saline) | uncultured bacterium | 39 | 0% |
| Sediment (saline) | Verrucomicrobia | 410560 | 2.98% |
| Sediment (saline) | WCHB1-60 | 527 | 0% |
| Sediment (saline) | WD272 | 650 | 0% |
| Sediment (saline) | Woesearchaeota (DHVEG-6) | 32339 | 0.23% |
| Soil (non-saline) | Acidobacteria | 2745324 | 19.61% |
| Soil (non-saline) | Actinobacteria | 1243107 | 8.88% |
| Soil (non-saline) | Aenigmarchaeota | 60 | 0% |
| Soil (non-saline) | Aerophobetes | 562 | 0% |
| Soil (non-saline) | Aigarchaeota | 4043 | 0.03% |
| Soil (non-saline) | Aminicenantes | 965 | 0.01% |
| Soil (non-saline) | aquifer1 | 56 | 0% |
| Soil (non-saline) | Aquificae | 15461 | 0.11% |
| Soil (non-saline) | Armatimonadetes | 50162 | 0.36% |
| Soil (non-saline) | Atribacteria | 174 | 0% |
| Soil (non-saline) | Bacteroidetes | 1567432 | 11.19% |
| Soil (non-saline) | Caldiserica | 4530 | 0.03% |
| Soil (non-saline) | Candidate division OP3 | 4211 | 0.03% |
| Soil (non-saline) | Candidate division SR1 | 440 | 0% |
| Soil (non-saline) | Chlamydiae | 8301 | 0.06% |
| Soil (non-saline) | Chlorobi | 46480 | 0.33% |
| Soil (non-saline) | Chloroflexi | 290621 | 2.08% |
| Soil (non-saline) | CKC4 | 2 | 0% |
| Soil (non-saline) | Cloacimonetes | 24 | 0% |
| Soil (non-saline) | Crenarchaeota | 17393 | 0.12% |
| Soil (non-saline) | Cyanobacteria | 108375 | 0.77% |
| Soil (non-saline) | Deferribacteres | 160 | 0% |
| Soil (non-saline) | Deinococcus-Thermus | 6083 | 0.04% |
| Soil (non-saline) | Diapherotrites | 1 | 0% |
| Soil (non-saline) | Dictyoglomi | 1 | 0% |
| Soil (non-saline) | Elusimicrobia | 27753 | 0.2% |
| Soil (non-saline) | Euryarchaeota | 17627 | 0.13% |
| Soil (non-saline) | Fibrobacteres | 7907 | 0.06% |
| Soil (non-saline) | Firmicutes | 713447 | 5.1% |
| Soil (non-saline) | Fusobacteria | 12458 | 0.09% |
| Soil (non-saline) | GAL08 | 44 | 0% |
| Soil (non-saline) | Gemmatimonadetes | 298450 | 2.13% |
| Soil (non-saline) | GOUTA4 | 477 | 0% |
| Soil (non-saline) | Gracilibacteria | 397 | 0% |
| Soil (non-saline) | Hyd24-12 | 1 | 0% |
| Soil (non-saline) | Hydrogenedentes | 2145 | 0.02% |
| Soil (non-saline) | JL-ETNP-Z39 | 1827 | 0.01% |
| Soil (non-saline) | Kazan-3B-09 | 7 | 0% |
| Soil (non-saline) | Latescibacteria | 31882 | 0.23% |
| Soil (non-saline) | Lentisphaerae | 3993 | 0.03% |
| Soil (non-saline) | Marine Hydrothermal Vent Group(MHVG) | 2 | 0% |
| Soil (non-saline) | Marinimicrobia (SAR406 clade) | 32 | 0% |
| Soil (non-saline) | Microgenomates | 1888 | 0.01% |
| Soil (non-saline) | Miscellaneous Crenarchaeotic Group | 3186 | 0.02% |
| Soil (non-saline) | Miscellaneous Euryarchaeotic Group(MEG) | 17 | 0% |
| Soil (non-saline) | Nitrospirae | 122150 | 0.87% |
| Soil (non-saline) | OC31 | 2 | 0% |
| Soil (non-saline) | Omnitrophica | 2620 | 0.02% |
| Soil (non-saline) | Parcubacteria | 3130 | 0.02% |
| Soil (non-saline) | Parvarchaeota | 56 | 0% |
| Soil (non-saline) | PAUC34f | 52 | 0% |
| Soil (non-saline) | Planctomycetes | 251808 | 1.8% |
| Soil (non-saline) | Proteobacteria | 4787424 | 34.19% |
| Soil (non-saline) | RsaHF231 | 3 | 0% |
| Soil (non-saline) | Saccharibacteria | 1394 | 0.01% |
| Soil (non-saline) | SHA-109 | 1093 | 0.01% |
| Soil (non-saline) | SM1K20 | 48 | 0% |
| Soil (non-saline) | SM2F11 | 2751 | 0.02% |
| Soil (non-saline) | Spirochaetae | 5463 | 0.04% |
| Soil (non-saline) | Synergistetes | 71 | 0% |
| Soil (non-saline) | TA06 | 769 | 0.01% |
| Soil (non-saline) | Tenericutes | 8464 | 0.06% |
| Soil (non-saline) | Thaumarchaeota | 96389 | 0.69% |
| Soil (non-saline) | Thermotogae | 827 | 0.01% |
| Soil (non-saline) | TM6 | 5761 | 0.04% |
| Soil (non-saline) | uncultured archaeon | 246 | 0% |
| Soil (non-saline) | Verrucomicrobia | 1442243 | 10.3% |
| Soil (non-saline) | WCHB1-60 | 3901 | 0.03% |
| Soil (non-saline) | WD272 | 26823 | 0.19% |
| Soil (non-saline) | Woesearchaeota (DHVEG-6) | 1264 | 0.01% |
| Surface (non-saline) | Acetothermia | 1847 | 0.02% |
| Surface (non-saline) | Acidobacteria | 614776 | 6.57% |
| Surface (non-saline) | Actinobacteria | 867881 | 9.28% |
| Surface (non-saline) | Aerophobetes | 329 | 0% |
| Surface (non-saline) | Aigarchaeota | 1262 | 0.01% |
| Surface (non-saline) | Aminicenantes | 255 | 0% |
| Surface (non-saline) | aquifer1 | 138 | 0% |
| Surface (non-saline) | Aquificae | 19316 | 0.21% |
| Surface (non-saline) | Armatimonadetes | 49233 | 0.53% |
| Surface (non-saline) | Atribacteria | 312 | 0% |
| Surface (non-saline) | Bacteroidetes | 648248 | 6.93% |
| Surface (non-saline) | Caldiserica | 871 | 0.01% |
| Surface (non-saline) | Calescamantes | 27 | 0% |
| Surface (non-saline) | Candidate division OP3 | 2401 | 0.03% |
| Surface (non-saline) | Candidate division SR1 | 5389 | 0.06% |
| Surface (non-saline) | Candidate division WS6 | 3 | 0% |
| Surface (non-saline) | Chlamydiae | 24467 | 0.26% |
| Surface (non-saline) | Chlorobi | 41754 | 0.45% |
| Surface (non-saline) | Chloroflexi | 175841 | 1.88% |
| Surface (non-saline) | CKC4 | 15 | 0% |
| Surface (non-saline) | Cloacimonetes | 8 | 0% |
| Surface (non-saline) | Crenarchaeota | 1 | 0% |
| Surface (non-saline) | Cyanobacteria | 480236 | 5.14% |
| Surface (non-saline) | Deferribacteres | 836 | 0.01% |
| Surface (non-saline) | Deinococcus-Thermus | 39626 | 0.42% |
| Surface (non-saline) | Diapherotrites | 96 | 0% |
| Surface (non-saline) | Dictyoglomi | 1 | 0% |
| Surface (non-saline) | Elusimicrobia | 3787 | 0.04% |
| Surface (non-saline) | Euryarchaeota | 5388 | 0.06% |
| Surface (non-saline) | Fibrobacteres | 607 | 0.01% |
| Surface (non-saline) | Firmicutes | 1145655 | 12.25% |
| Surface (non-saline) | Fusobacteria | 60652 | 0.65% |
| Surface (non-saline) | GAL08 | 85 | 0% |
| Surface (non-saline) | Gemmatimonadetes | 69596 | 0.74% |
| Surface (non-saline) | GOUTA4 | 119 | 0% |
| Surface (non-saline) | Gracilibacteria | 2848 | 0.03% |
| Surface (non-saline) | Hyd24-12 | 49 | 0% |
| Surface (non-saline) | Hydrogenedentes | 2173 | 0.02% |
| Surface (non-saline) | JL-ETNP-Z39 | 210 | 0% |
| Surface (non-saline) | Kazan-3B-09 | 16 | 0% |
| Surface (non-saline) | Latescibacteria | 21691 | 0.23% |
| Surface (non-saline) | LCP-89 | 58 | 0% |
| Surface (non-saline) | Lentisphaerae | 3243 | 0.03% |
| Surface (non-saline) | Marinimicrobia (SAR406 clade) | 123 | 0% |
| Surface (non-saline) | Microgenomates | 1006 | 0.01% |
| Surface (non-saline) | Miscellaneous Crenarchaeotic Group | 26 | 0% |
| Surface (non-saline) | Miscellaneous Euryarchaeotic Group(MEG) | 495 | 0.01% |
| Surface (non-saline) | Nitrospirae | 148422 | 1.59% |
| Surface (non-saline) | OC31 | 5 | 0% |
| Surface (non-saline) | Omnitrophica | 1408 | 0.02% |
| Surface (non-saline) | Parcubacteria | 3071 | 0.03% |
| Surface (non-saline) | Parvarchaeota | 9 | 0% |
| Surface (non-saline) | PAUC34f | 213 | 0% |
| Surface (non-saline) | Planctomycetes | 169615 | 1.81% |
| Surface (non-saline) | Proteobacteria | 4195241 | 44.86% |
| Surface (non-saline) | RsaHF231 | 1 | 0% |
| Surface (non-saline) | S2R-29 | 1657 | 0.02% |
| Surface (non-saline) | Saccharibacteria | 460 | 0% |
| Surface (non-saline) | SHA-109 | 494 | 0.01% |
| Surface (non-saline) | SM1K20 | 1 | 0% |
| Surface (non-saline) | SM2F11 | 1416 | 0.02% |
| Surface (non-saline) | Spirochaetae | 1937 | 0.02% |
| Surface (non-saline) | Synergistetes | 67 | 0% |
| Surface (non-saline) | TA06 | 4826 | 0.05% |
| Surface (non-saline) | Tenericutes | 285008 | 3.05% |
| Surface (non-saline) | Thaumarchaeota | 35957 | 0.38% |
| Surface (non-saline) | Thermodesulfobacteria | 4 | 0% |
| Surface (non-saline) | Thermotogae | 11029 | 0.12% |
| Surface (non-saline) | TM6 | 6330 | 0.07% |
| Surface (non-saline) | uncultured archaeon | 1 | 0% |
| Surface (non-saline) | Verrucomicrobia | 189643 | 2.03% |
| Surface (non-saline) | WCHB1-60 | 421 | 0% |
| Surface (non-saline) | WD272 | 152 | 0% |
| Surface (non-saline) | Woesearchaeota (DHVEG-6) | 610 | 0.01% |
| Surface (saline) | Acetothermia | 8257 | 0.05% |
| Surface (saline) | Acidobacteria | 160810 | 0.9% |
| Surface (saline) | Actinobacteria | 586234 | 3.28% |
| Surface (saline) | Aenigmarchaeota | 24 | 0% |
| Surface (saline) | Aerophobetes | 435 | 0% |
| Surface (saline) | Aminicenantes | 1391 | 0.01% |
| Surface (saline) | Ancient Archaeal Group(AAG) | 2 | 0% |
| Surface (saline) | aquifer1 | 45 | 0% |
| Surface (saline) | Aquificae | 12605 | 0.07% |
| Surface (saline) | Armatimonadetes | 14484 | 0.08% |
| Surface (saline) | Atribacteria | 3530 | 0.02% |
| Surface (saline) | Bacteroidetes | 2444346 | 13.66% |
| Surface (saline) | Caldiserica | 22 | 0% |
| Surface (saline) | Candidate division OP3 | 6423 | 0.04% |
| Surface (saline) | Candidate division SR1 | 1490 | 0.01% |
| Surface (saline) | Chlamydiae | 962 | 0.01% |
| Surface (saline) | Chlorobi | 21168 | 0.12% |
| Surface (saline) | Chloroflexi | 95925 | 0.54% |
| Surface (saline) | CKC4 | 5 | 0% |
| Surface (saline) | Cloacimonetes | 723 | 0% |
| Surface (saline) | Cyanobacteria | 2678289 | 14.97% |
| Surface (saline) | Deferribacteres | 12332 | 0.07% |
| Surface (saline) | Deinococcus-Thermus | 5101 | 0.03% |
| Surface (saline) | Diapherotrites | 7 | 0% |
| Surface (saline) | Dictyoglomi | 10 | 0% |
| Surface (saline) | Elusimicrobia | 1933 | 0.01% |
| Surface (saline) | Euryarchaeota | 12863 | 0.07% |
| Surface (saline) | Fibrobacteres | 2937 | 0.02% |
| Surface (saline) | Firmicutes | 1200575 | 6.71% |
| Surface (saline) | Fusobacteria | 22255 | 0.12% |
| Surface (saline) | Gemmatimonadetes | 31259 | 0.17% |
| Surface (saline) | GOUTA4 | 38 | 0% |
| Surface (saline) | Gracilibacteria | 12179 | 0.07% |
| Surface (saline) | Hyd24-12 | 453 | 0% |
| Surface (saline) | Hydrogenedentes | 2088 | 0.01% |
| Surface (saline) | JL-ETNP-Z39 | 290 | 0% |
| Surface (saline) | Kazan-3B-09 | 107 | 0% |
| Surface (saline) | Latescibacteria | 13076 | 0.07% |
| Surface (saline) | LCP-89 | 52 | 0% |
| Surface (saline) | LD1-PA38 | 80 | 0% |
| Surface (saline) | Lentisphaerae | 29810 | 0.17% |
| Surface (saline) | Marine Hydrothermal Vent Group(MHVG) | 33 | 0% |
| Surface (saline) | Marinimicrobia (SAR406 clade) | 5087 | 0.03% |
| Surface (saline) | Microgenomates | 288 | 0% |
| Surface (saline) | Miscellaneous Crenarchaeotic Group | 429 | 0% |
| Surface (saline) | Miscellaneous Euryarchaeotic Group(MEG) | 3 | 0% |
| Surface (saline) | Nitrospirae | 154614 | 0.86% |
| Surface (saline) | OC31 | 19 | 0% |
| Surface (saline) | Omnitrophica | 32428 | 0.18% |
| Surface (saline) | Parcubacteria | 7031 | 0.04% |
| Surface (saline) | Parvarchaeota | 7 | 0% |
| Surface (saline) | PAUC34f | 1307 | 0.01% |
| Surface (saline) | Planctomycetes | 389389 | 2.18% |
| Surface (saline) | Proteobacteria | 9387089 | 52.47% |
| Surface (saline) | RsaHF231 | 2 | 0% |
| Surface (saline) | Saccharibacteria | 191 | 0% |
| Surface (saline) | SHA-109 | 1912 | 0.01% |
| Surface (saline) | SM1K20 | 7 | 0% |
| Surface (saline) | SM2F11 | 436 | 0% |
| Surface (saline) | Spirochaetae | 11773 | 0.07% |
| Surface (saline) | Synergistetes | 311 | 0% |
| Surface (saline) | TA06 | 890 | 0% |
| Surface (saline) | Tenericutes | 3870 | 0.02% |
| Surface (saline) | Thaumarchaeota | 34129 | 0.19% |
| Surface (saline) | Thermotogae | 118 | 0% |
| Surface (saline) | TM6 | 2907 | 0.02% |
| Surface (saline) | uncultured archaeon | 225 | 0% |
| Surface (saline) | Verrucomicrobia | 464163 | 2.59% |
| Surface (saline) | WCHB1-60 | 1621 | 0.01% |
| Surface (saline) | WD272 | 22 | 0% |
| Surface (saline) | Woesearchaeota (DHVEG-6) | 6211 | 0.03% |
| Water (non-saline) | Acetothermia | 198 | 0% |
| Water (non-saline) | Acidobacteria | 366560 | 1.81% |
| Water (non-saline) | Actinobacteria | 3250148 | 16.05% |
| Water (non-saline) | Aenigmarchaeota | 147 | 0% |
| Water (non-saline) | Aerophobetes | 192 | 0% |
| Water (non-saline) | Aminicenantes | 18375 | 0.09% |
| Water (non-saline) | aquifer1 | 89 | 0% |
| Water (non-saline) | Armatimonadetes | 33499 | 0.17% |
| Water (non-saline) | Atribacteria | 660 | 0% |
| Water (non-saline) | Bacteroidetes | 3422394 | 16.9% |
| Water (non-saline) | Caldiserica | 145 | 0% |
| Water (non-saline) | Candidate division OP3 | 22010 | 0.11% |
| Water (non-saline) | Candidate division SR1 | 2431 | 0.01% |
| Water (non-saline) | Chlamydiae | 8676 | 0.04% |
| Water (non-saline) | Chlorobi | 112650 | 0.56% |
| Water (non-saline) | Chloroflexi | 350766 | 1.73% |
| Water (non-saline) | CKC4 | 221 | 0% |
| Water (non-saline) | Cloacimonetes | 1465 | 0.01% |
| Water (non-saline) | Crenarchaeota | 258 | 0% |
| Water (non-saline) | Cyanobacteria | 2945876 | 14.55% |
| Water (non-saline) | Deferribacteres | 1791 | 0.01% |
| Water (non-saline) | Deinococcus-Thermus | 2509 | 0.01% |
| Water (non-saline) | Diapherotrites | 68 | 0% |
| Water (non-saline) | Dictyoglomi | 7 | 0% |
| Water (non-saline) | Elusimicrobia | 13723 | 0.07% |
| Water (non-saline) | Euryarchaeota | 28563 | 0.14% |
| Water (non-saline) | Fibrobacteres | 4194 | 0.02% |
| Water (non-saline) | Firmicutes | 467255 | 2.31% |
| Water (non-saline) | Fusobacteria | 15785 | 0.08% |
| Water (non-saline) | GAL08 | 65 | 0% |
| Water (non-saline) | Gemmatimonadetes | 56677 | 0.28% |
| Water (non-saline) | GOUTA4 | 586 | 0% |
| Water (non-saline) | Gracilibacteria | 4122 | 0.02% |
| Water (non-saline) | Hyd24-12 | 258 | 0% |
| Water (non-saline) | Hydrogenedentes | 1072 | 0.01% |
| Water (non-saline) | JL-ETNP-Z39 | 28 | 0% |
| Water (non-saline) | Kazan-3B-09 | 283 | 0% |
| Water (non-saline) | Latescibacteria | 11411 | 0.06% |
| Water (non-saline) | LCP-89 | 218 | 0% |
| Water (non-saline) | Lentisphaerae | 12794 | 0.06% |
| Water (non-saline) | Marine Hydrothermal Vent Group(MHVG) | 6 | 0% |
| Water (non-saline) | Marinimicrobia (SAR406 clade) | 3385 | 0.02% |
| Water (non-saline) | Microgenomates | 2700 | 0.01% |
| Water (non-saline) | Miscellaneous Crenarchaeotic Group | 16909 | 0.08% |
| Water (non-saline) | Miscellaneous Euryarchaeotic Group(MEG) | 92 | 0% |
| Water (non-saline) | Nitrospirae | 41006 | 0.2% |
| Water (non-saline) | OC31 | 78 | 0% |
| Water (non-saline) | Omnitrophica | 12577 | 0.06% |
| Water (non-saline) | Parcubacteria | 28041 | 0.14% |
| Water (non-saline) | Parvarchaeota | 362 | 0% |
| Water (non-saline) | PAUC34f | 438 | 0% |
| Water (non-saline) | Planctomycetes | 360535 | 1.78% |
| Water (non-saline) | Proteobacteria | 7777792 | 38.41% |
| Water (non-saline) | RsaHF231 | 30 | 0% |
| Water (non-saline) | Saccharibacteria | 3273 | 0.02% |
| Water (non-saline) | SHA-109 | 631 | 0% |
| Water (non-saline) | SM1K20 | 716 | 0% |
| Water (non-saline) | SM2F11 | 5414 | 0.03% |
| Water (non-saline) | Spirochaetae | 16512 | 0.08% |
| Water (non-saline) | Synergistetes | 211 | 0% |
| Water (non-saline) | TA06 | 1999 | 0.01% |
| Water (non-saline) | Tenericutes | 1191 | 0.01% |
| Water (non-saline) | Thaumarchaeota | 16940 | 0.08% |
| Water (non-saline) | Thermotogae | 84 | 0% |
| Water (non-saline) | TM6 | 6917 | 0.03% |
| Water (non-saline) | uncultured archaeon | 12 | 0% |
| Water (non-saline) | Verrucomicrobia | 779446 | 3.85% |
| Water (non-saline) | WCHB1-60 | 6159 | 0.03% |
| Water (non-saline) | WD272 | 188 | 0% |
| Water (non-saline) | Woesearchaeota (DHVEG-6) | 4952 | 0.02% |
| Water (saline) | Acetothermia | 263 | 0% |
| Water (saline) | Acidobacteria | 468181 | 2.9% |
| Water (saline) | Actinobacteria | 542563 | 3.36% |
| Water (saline) | Aenigmarchaeota | 19 | 0% |
| Water (saline) | Aerophobetes | 155 | 0% |
| Water (saline) | Aigarchaeota | 4 | 0% |
| Water (saline) | Aminicenantes | 1776 | 0.01% |
| Water (saline) | Ancient Archaeal Group(AAG) | 2 | 0% |
| Water (saline) | aquifer1 | 1 | 0% |
| Water (saline) | Aquificae | 4 | 0% |
| Water (saline) | Armatimonadetes | 1265 | 0.01% |
| Water (saline) | Atribacteria | 706 | 0% |
| Water (saline) | Bacteroidetes | 3730714 | 23.09% |
| Water (saline) | Caldiserica | 227 | 0% |
| Water (saline) | Candidate division OP3 | 6202 | 0.04% |
| Water (saline) | Candidate division SR1 | 118 | 0% |
| Water (saline) | Chlamydiae | 1017 | 0.01% |
| Water (saline) | Chlorobi | 20001 | 0.12% |
| Water (saline) | Chloroflexi | 133382 | 0.83% |
| Water (saline) | CKC4 | 12 | 0% |
| Water (saline) | Cloacimonetes | 8368 | 0.05% |
| Water (saline) | Crenarchaeota | 57 | 0% |
| Water (saline) | Cyanobacteria | 2059139 | 12.74% |
| Water (saline) | Deferribacteres | 4514 | 0.03% |
| Water (saline) | Deinococcus-Thermus | 774 | 0% |
| Water (saline) | Diapherotrites | 15 | 0% |
| Water (saline) | Dictyoglomi | 11 | 0% |
| Water (saline) | Elusimicrobia | 836 | 0.01% |
| Water (saline) | Euryarchaeota | 115673 | 0.72% |
| Water (saline) | Fibrobacteres | 1228 | 0.01% |
| Water (saline) | Firmicutes | 63649 | 0.39% |
| Water (saline) | Fusobacteria | 33730 | 0.21% |
| Water (saline) | GAL08 | 10 | 0% |
| Water (saline) | Gemmatimonadetes | 14309 | 0.09% |
| Water (saline) | GOUTA4 | 106 | 0% |
| Water (saline) | Gracilibacteria | 2284 | 0.01% |
| Water (saline) | Hyd24-12 | 1725 | 0.01% |
| Water (saline) | Hydrogenedentes | 588 | 0% |
| Water (saline) | JL-ETNP-Z39 | 155 | 0% |
| Water (saline) | Kazan-3B-09 | 384 | 0% |
| Water (saline) | Latescibacteria | 5747 | 0.04% |
| Water (saline) | LCP-89 | 518 | 0% |
| Water (saline) | LD1-PA38 | 2 | 0% |
| Water (saline) | Lentisphaerae | 6995 | 0.04% |
| Water (saline) | Marine Hydrothermal Vent Group(MHVG) | 23 | 0% |
| Water (saline) | Marinimicrobia (SAR406 clade) | 329714 | 2.04% |
| Water (saline) | Microgenomates | 180 | 0% |
| Water (saline) | Miscellaneous Crenarchaeotic Group | 1505 | 0.01% |
| Water (saline) | Miscellaneous Euryarchaeotic Group(MEG) | 3 | 0% |
| Water (saline) | Nitrospirae | 10304 | 0.06% |
| Water (saline) | OC31 | 23 | 0% |
| Water (saline) | Omnitrophica | 921 | 0.01% |
| Water (saline) | Parcubacteria | 1125 | 0.01% |
| Water (saline) | Parvarchaeota | 26 | 0% |
| Water (saline) | PAUC34f | 4057 | 0.03% |
| Water (saline) | Planctomycetes | 105276 | 0.65% |
| Water (saline) | Proteobacteria | 7981764 | 49.4% |
| Water (saline) | RsaHF231 | 3 | 0% |
| Water (saline) | Saccharibacteria | 766 | 0% |
| Water (saline) | SBYG-2791 | 16 | 0% |
| Water (saline) | SHA-109 | 331 | 0% |
| Water (saline) | SM1K20 | 45 | 0% |
| Water (saline) | SM2F11 | 79 | 0% |
| Water (saline) | Spirochaetae | 15085 | 0.09% |
| Water (saline) | Synergistetes | 76 | 0% |
| Water (saline) | TA06 | 2482 | 0.02% |
| Water (saline) | Tenericutes | 2469 | 0.02% |
| Water (saline) | Thaumarchaeota | 93841 | 0.58% |
| Water (saline) | Thermotogae | 49 | 0% |
| Water (saline) | TM6 | 1515 | 0.01% |
| Water (saline) | uncultured archaeon | 19 | 0% |
| Water (saline) | Verrucomicrobia | 376298 | 2.33% |
| Water (saline) | WCHB1-60 | 41 | 0% |
| Water (saline) | WD272 | 256 | 0% |
| Water (saline) | Woesearchaeota (DHVEG-6) | 1609 | 0.01% |
# save summary table
taxa_sum_df %>%
filter(Abundance != 0) %>%
write.csv(file = paste0("EMP_", Grouping_var,"_", Rank,".csv"))Plot a heatmap
# Agglomerate taxa
EMP_merge %>%
tax_glom(Rank, NArm = TRUE) %>%
transform_sample_counts(function(x) x / sum(x) * 100) ->
Ps_obj_filt_glom
plot_heatmap(
Ps_obj_filt_glom,
# method = "NMDS",
# distance = "bray",
trans = log_trans(4),
sample.order = Grouping_var,
sample.label = Grouping_var,
taxa.label = Rank,
taxa.order = Rank_order$OTU
) +
theme_bw(base_size = 18) +
theme(axis.text.x = element_text(angle = 45.0, vjust = 1, hjust = 1)) +
scale_fill_viridis(trans = "log", labels = scales::number_format(accuracy = 0.1), option = "magma", na.value = "black") +
labs(fill = "Abundance (%)")
Plot a bar chart
EMP_merge %>%
tax_glom(., Rank) %>%
transform_sample_counts(., function(x) x / sum(x) * 100) %>%
psmelt() %>%
mutate_if(is.character, as.factor) %>%
mutate(Phylum = fct_relevel(pull(., Rank), rev(unique(pull(Rank_order, Rank))))) %>%
ggplot(aes(fill = !!sym(Rank), x = !!sym(Grouping_var), y = log10(Abundance))) +
geom_col() +
theme_set(theme_bw()) +
theme(axis.text.x = element_text(angle = 45.0, vjust = 1, hjust = 1),
legend.position = "bottom") +
labs(y = "Log10 rel. abundance") +
facet_wrap(~get(Rank), ncol = 5) 
Plot a violin and dot chart
EMP %>%
tax_glom(., Rank) %>%
transform_sample_counts(., function(x) x / sum(x) * 100) %>%
psmelt() %>%
mutate_if(is.character, as.factor) %>%
mutate(Taxa = fct_relevel(pull(., Rank), rev(unique(pull(Rank_order, Rank))))) %>%
mutate(Taxa = fct_other(Taxa, drop = pull(Rank_order, Rank)[Rank_order$Abundance < 0.1], other_level = "Rare")) %>%
ggplot(aes(x = Taxa, y = Abundance)) +
geom_violin(aes(group = interaction(Taxa, !!sym(Grouping_var))),
scale = "width") +
geom_point2(aes(colour = Taxa),
position = position_jitter(width = 0.2),
alpha = 1/4,
stroke = 0,
size = 2) +
theme(axis.text = element_text(angle = 45.0),
axis.text.x = element_text(vjust = 1, hjust = 1) ) +
# scale_fill_locuszoom() +
# scale_color_manual(values = pal("d3js")[c(3, 4, 2)]) +
labs(x = NULL, y = "Abundance (%)", colour = Rank) +
guides(colour = guide_legend(override.aes = list(size = 5, alpha = 1))) +
facet_wrap(~get(Grouping_var), ncol = 2) 
Generate heat-tree plots using Metacoder (Foster, Sharpton, and Grünwald 2017)
# Convert phyloseq to taxmap
EMP %>%
# transform_sample_counts(function(x) x / sum(x) ) %>% # not really needed
parse_phyloseq() %>%
taxa::filter_taxa(., !taxon_ranks %in% c("Species", "Genus", "Family", "Order")) -> # tips will be Class
EMP_taxmap
# Potentially drop out low reads
# EMP_taxmap$data$otu_table <- zero_low_counts(EMP_taxmap, "otu_table", min_count = 5)
# no_reads <- rowSums(EMP_taxmap$data$otu_table[, EMP_taxmap$data$sample_data$sample_id]) == 0
# EMP_taxmap <- filter_obs(EMP_taxmap, data = "tax_data", ! no_reads, drop_taxa = TRUE)
# Sum counts per group
EMP_taxmap$data$tax_counts <- calc_taxon_abund(EMP_taxmap,
data = 'otu_table',
cols = EMP_taxmap$data$sample_data$sample_id,
groups = pull(EMP_taxmap$data$sample_data, Grouping_var))
# Generate a plot for each group
my_plots <- lapply(sort(unique(get_variable(EMP, Grouping_var))), function(group) {
# do something with time point data
set.seed(2020) # Make each plot layout look the same if using another layout
EMP_taxmap %>%
heat_tree(.,
node_label = taxon_names,
node_size = n_obs,
node_color = EMP_taxmap$data$tax_counts[[group]],
node_size_axis_label = 'OTU count',
node_color_axis_label = 'Sequence count',
layout = "automatic",
node_size_range = c(0.013, 0.04), # makes scale range the same in both
title = group)
})
wrap_plots(my_plots, ncol = 3)